Surface rendering of the virus particle (top left):
These images describe the shapes and placement of viral capsid proteins and
the relief of the capsid surface. All of the images are calculated from atomic
coordinates in the VIPER database.
The Chimera
renderings use multiple colors to delineate the subunits and lighting to
provide a 3-dimensional appearance. Viruses with similar capsid organization
are colored in the same way.
The GRASP drawing
(depth-cued) based on the atomic coordinates of the viral capsid proteins.
The colors are depth cued along a monochromic spectrum with lighter brown at a larger radius,
and darker brown as the radius decreases. This rendering is designed to give an impression similar
to that of a cryo electron miscroscopy reconstruction at 20 Å resolution. The
surface topology is readily seen with large-scale features such as "canyons", "mountain
tops", and distinctive morphological units (e.g. hexamers and pentamers) readily visible.
It is convenient to compare virus particles with this rendering because if you click
on the image, an image appears that is scaled with all other viruses that are presented
in the site. Thus it is possible to create a gallery of viruses that are scaled to
each other by combining these images for all the viruses. Visit
Visual VIPER to easily create such a gallery.
Ribbon drawing of the subunit(s) (lower left):
A ribbon drawing is provided for each of the unique gene products in the viral capsid.
For a quasi-equivalent virus made of multiple copies of a single gene product, only one
of the copies is shown. For picornavirus and related capsids there will be three
ß sandwich domains. The ribbon drawings are colored with tones changing
continuously through the spectrum from blue at the N-terminus to red at the C-terminus.
Strands of ß-sheets are depicted as arrows pointing in the direction of increasing
sequence and helices are formed as coiled ribbons. Regions without a distinct secondary
structure are depicted as a tube.
Geometric description of the capsid (upper right):
All of the viral capsids in this database display icosahedral symmetry. Some of the particles
have the shape of an icosahedron, while others conform to the shape of other geometric solids
that display icosahedral symmetry. These may include a truncated icosahedron, a
rhombic triacontahedron, or a dodecahedron. The geometric figure shown with each virus
was found to best describe the geometry of the subunit interactions. The fidelity of
some viruses to these shapes is remarkable with dihedral angles between subunits conforming
to within experimental error to the dihedral angles required to form the geometric solid.
Capsomeres depicted as C-alpha drawings of subunits (bottom right):
This drawing shows the detailed association of subunit C-alpha backbones to illustrate
the dominant interactions within the particle. A portion of the geometric figure
shown in the upper right is filled in with viral subunits to illustrate the relationship
between chemistry and geometry that exists in these remarkable assemblies.
Surface rendering of the virus particle (top left):
These images describe the shapes and placement of viral capsid proteins and
the relief of the capsid surface. All of the images are calculated from atomic
coordinates in the VIPER database.
The 
Ribbon drawing of the subunit(s) (lower left):
A ribbon drawing is provided for each of the unique gene products in the viral capsid.
For a quasi-equivalent virus made of multiple copies of a single gene product, only one
of the copies is shown. For picornavirus and related capsids there will be three
ß sandwich domains. The ribbon drawings are colored with tones changing
continuously through the spectrum from blue at the N-terminus to red at the C-terminus.
Strands of ß-sheets are depicted as arrows pointing in the direction of increasing
sequence and helices are formed as coiled ribbons. Regions without a distinct secondary
structure are depicted as a tube.
Geometric description of the capsid (upper right):
All of the viral capsids in this database display icosahedral symmetry. Some of the particles
have the shape of an icosahedron, while others conform to the shape of other geometric solids
that display icosahedral symmetry. These may include a truncated icosahedron, a
rhombic triacontahedron, or a dodecahedron. The geometric figure shown with each virus
was found to best describe the geometry of the subunit interactions. The fidelity of
some viruses to these shapes is remarkable with dihedral angles between subunits conforming
to within experimental error to the dihedral angles required to form the geometric solid.
Capsomeres depicted as C-alpha drawings of subunits (bottom right):
This drawing shows the detailed association of subunit C-alpha backbones to illustrate
the dominant interactions within the particle. A portion of the geometric figure
shown in the upper right is filled in with viral subunits to illustrate the relationship
between chemistry and geometry that exists in these remarkable assemblies.